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Researcher's Guide to Finding Molecular Biology Data: Structure

RCSB Protein Data Bank (PDB)

Access RCSB PDB

What is it?

  • Worldwide repository for information about 3D structures of biological macromolecules e.g. ribosomes
  • Provides tools for structure visualization
  • Research Collaboratory for Structural Bioinformatics (RCSB) manages RCSB PDB
    • Staff located at Rutgers University and University of California, San Diego
    • A deposition, processing and distribution center for Worldwide Protein Data Bank (wwPDB)
  • RCSB PDB built using PDB archive, which is maintained by wwPDB
    • Archive updated weekly

Access

  • Public access
  • Data files in RCSB PDB archive are free of all copyright restrictions
  • Molecule of the Month illustrations and articles are copyrighted
  • All other articles and text on the site are copyrighted
  • For further information on use of RCSB PDB materials, visit RCSB PDB Policies & References

How to Retrieve Data

  • Searching
    • Where to start
      • To search for structures, enter keyword or PDB ID into search box at the top of homepage
      •  Click on Author button above search box to search by author name
    • Multiple search and browse options available, for more information, visit Searching the RCSB PDB
  •  Multiple options available for download of data files, including maintaining a local copy of all PDB files
    • For more information, select options from the Tool box in the right menu on the RCSB PDB homepage

Submissions

  • Accepts all experimentally determined structures that meet minimum requirements
    • Three dimensional coordinates
    • Information about composition of structure
    • Information about experiment performed
    • Details of structure determination steps
    • Author contact information
  • Types of structures accepted:
    • Polypeptides and their complexes
      • All gene products
      • All naturally-occurring peptides that are non-ribosomal in origin
      • All peptidic repeat units of larger polymers
      • Synthetic peptides with at least 24 residues in a polymer chain
    • Polynucleotides of 4 or more residues, and their complexes
    • Polysaccharides of 4 or more residues, and their complexes
  •  RCSB PDB has several tools for the validation and deposition of data, visit RCSB PDB Data Validation & Deposition Services for more information
  •  Length of time structure held from public release selected during deposition

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Cambridge Structural Database (CSD)

Access CSD

What is it?

  • Repository of small-molecule organic and metal-organic crystal structures compiled by the Cambridge Crystallographic Data Centre (CCDC), a company that started at the University of Cambridge
  • Data from:
    • Publications
    • Private communications via direct deposit
  • Does not store:
    • Polypeptides and polysaccharides
    • Oligonucleotides
    • Inorganic structures
    • Metals and alloys
  • Part of the CSD System, which includes software for:
    • Search and information retrieval
    • Structure visualization
    • Statistical analysis of retrieved data
    • Knowledge bases derived from CSD

Access

  • Anyone can request data for bona fide research purposes
  • CSD System must be purchased

How to Retrieve Data

  • May request data after associated paper has been published
    • Use online Request Form
    • One paper per request
    • Need full journal citation and CCDC Deposition Number, which should be in paper
    • Data sent in CIF format free of charge
  • Currently only data published after 1994 is available via request
  • Data published before 1994 is available through CSD distributed with CSD System (see above for access instructions)

Submissions

  • Accepts crystal structure data from X-ray, neutron diffraction and powder studies using a constrained refinement for:
    • Organic compounds
    • Metal-organic compounds
    • Metal carbonyls
    • Boron compounds containing one or more B-H or B-OH bond and borazines
    • Ring compounds containing any two of the following elements: N, P, S, Se and Te
  • Types of depositions:
    • Pre-publication
    • Published
    • Private communication: structure not intended for publication
  • For further information, visit Deposit a Structure

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